Every Day UNIX and Working with Hoffman - Revision history

Dmargolis: /* How do I switch FSL Versions? */

2017-07-08T14:22:24Z

How do I switch FSL Versions?

← Older revision		Revision as of 14:22, 8 July 2017
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	===How do I switch FSL Versions?===		===How do I switch FSL Versions?===
	Please see the help output of the following utility on hoffman which eases this process:		Please see [[Hoffman2:Modules]] for more information on switching FSL versions.
			<!--Please see the help output of the following utility on hoffman which eases this process:
	$ switch_fsl --help		$ switch_fsl --help
	Description: switch_fsl easily and cleanly switches between various fsl versions.		Description: switch_fsl easily and cleanly switches between various fsl versions.
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	switch_fsl --switch 4.0.4		switch_fsl --switch 4.0.4
	switch_fsl -h		switch_fsl -h
	switch_fsl --check		switch_fsl --check-->



	==External Links==		==External Links==

Dmargolis at 20:24, 26 May 2017

2017-05-26T20:24:47Z

← Older revision		Revision as of 20:24, 26 May 2017
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	==Setting up your Bash Profile==		==Setting up your Bash Profile==
	How to ~~get~~ access to CCN-supported software.		How to set up your Bash Profile to access CCN-supported software.
	: [[Hoffman2:Modules]]		: [[Hoffman2:Modules]]
	<!-- This is the easiest part. Just place this one, single line in your ~/.bash_profile:		<!-- This is the easiest part. Just place this one, single line in your ~/.bash_profile:

Dmargolis: /* SPM */

2017-05-26T20:06:24Z

SPM

← Older revision		Revision as of 20:06, 26 May 2017
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	==SPM==		==SPM==
	SPM8 as well as the older SPM5 are on hoffman. In order to use these, you must add the path ("Add with Subfolders") in MATLAB.		SPM8 as well as the older SPM5 are on hoffman. In order to use these, you must add the path ("Add with Subfolders") in MATLAB.

			The path to spm12 is:
			/u/project/CCN/apps/spm12

	The path to spm8 is:		The path to spm8 is:
	/u/~~home~~/~~FMRI~~/apps/spm8		/u/project/CCN/apps/spm8

	Likewise, the path to spm5 is:		Likewise, the path to spm5 is:
	/u/~~home~~/~~FMRI~~/apps/spm5		/u/project/CCN/apps/spm5



	==FAQ==		==FAQ==

Dmargolis: /* Setting up your Bash Profile */

2017-05-26T20:04:41Z

Setting up your Bash Profile

← Older revision		Revision as of 20:04, 26 May 2017
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	==Setting up your Bash Profile==		==Setting up your Bash Profile==
	This is the easiest part. Just place this one, single line in your ~/.bash_profile:		How to get access to CCN-supported software.
			: [[Hoffman2:Modules]]
			<!-- This is the easiest part. Just place this one, single line in your ~/.bash_profile:
	source /u/home/FMRI/apps/etc/profile		source /u/home/FMRI/apps/etc/profile

Line 127:		Line 129:
	umask 007		umask 007

	Save, then log out and back in. This is all that is needed to gain full access to all FMRI applications. Nothing else should be put in this file, ever, unless you 100% know what you are doing and why, don't take someone else's word for it either.		Save, then log out and back in. This is all that is needed to gain full access to all FMRI applications. Nothing else should be put in this file, ever, unless you 100% know what you are doing and why, don't take someone else's word for it either. -->



	==Cyberduck: An SFTP client==		==Cyberduck: An SFTP client==

Ccn admin: 33 revisions

2014-01-16T03:13:38Z

33 revisions

← Older revision	Revision as of 03:13, 16 January 2014
(No difference)

Elau at 23:40, 13 March 2012

2012-03-13T23:40:22Z

← Older revision		Revision as of 23:40, 13 March 2012
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	A [http://www.tfug.org/helpdesk/general/man.html Beginners Guide to man Pages] is an excellent introduction into how to move around a man page easily and understand what it's telling you.		A [http://www.tfug.org/helpdesk/general/man.html Beginners Guide to man Pages] is an excellent introduction into how to move around a man page easily and understand what it's telling you.

	=Setting up your Bash Profile=

			==Setting up your Bash Profile==
	This is the easiest part. Just place this one, single line in your ~/.bash_profile:		This is the easiest part. Just place this one, single line in your ~/.bash_profile:
	source /u/home/FMRI/apps/etc/profile		source /u/home/FMRI/apps/etc/profile

Elau: /* The Trifecta of Every Day Unix */

2012-03-13T23:39:46Z

The Trifecta of Every Day Unix

← Older revision		Revision as of 23:39, 13 March 2012
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	# File System Navigation		# File System Navigation
	# File & Shell Management		# File & Shell Management
			# Learning to Fish or The Man Pages

	Each of these areas require knowledge of a few small programs and how they behave. In the following sections, each program and utility is covered in detail. When appropriate, a link to the relevant wiki page on the topic is provided.		Each of these areas require knowledge of a few small programs and how they behave. In the following sections, each program and utility is covered in detail. When appropriate, a link to the relevant wiki page on the topic is provided.
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	Where appropriate, links to external tutorials deemed suitable and apropriate to the topic are provided rather than reproducing the work here.		Where appropriate, links to external tutorials deemed suitable and apropriate to the topic are provided rather than reproducing the work here.

	~~===Learning to Fish or The Man Pages===~~
	However, possibly even more important is being able to find information on one's own. In the spirit of this, the instructional is concluded with a detailed coverage of the built-in unix manual pages. Virtually every program installed on a UNIX like system provied a manual page for reference. Even the most proficient of UNIX users could never retain the dizzying array of programs and their options in their working memory and with the built-in manual pages, they'll never need to.

	~~The man pages (for ''manual'') are the be all end all reference on UNIX systems. When reading a man page becomes natural, you know there is nothing you can't get done quickly and efficiently.~~

	~~A [http://www.tfug.org/helpdesk/general/man.html Beginners Guide to man Pages] is an excellent introduction into how to move around a man page easily and understand what it's telling you.~~


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	#Find all files owned by user 'foo' and change their permissions		#Find all files owned by user 'foo' and change their permissions
	$ find . -type f -user foo -exec chmod -R ug+rwX {} \;		$ find . -type f -user foo -exec chmod -R ug+rwX {} \;


			===Learning to Fish or The Man Pages===
			However, possibly even more important is being able to find information on one's own. In the spirit of this, the instructional is concluded with a detailed coverage of the built-in unix manual pages. Virtually every program installed on a UNIX like system provied a manual page for reference. Even the most proficient of UNIX users could never retain the dizzying array of programs and their options in their working memory and with the built-in manual pages, they'll never need to.

			The man pages (for ''manual'') are the be all end all reference on UNIX systems. When reading a man page becomes natural, you know there is nothing you can't get done quickly and efficiently.

			A [http://www.tfug.org/helpdesk/general/man.html Beginners Guide to man Pages] is an excellent introduction into how to move around a man page easily and understand what it's telling you.

	=Setting up your Bash Profile=		=Setting up your Bash Profile=

Elau at 23:34, 13 March 2012

2012-03-13T23:34:35Z

← Older revision		Revision as of 23:34, 13 March 2012
Line 1:		Line 1:
	=The Trifecta of Every Day Unix=		==The Trifecta of Every Day Unix==
	Working with UNIX and UNIX like systems via the command line can be intimidating. The good news is a normal user only needs to have a firm understanding of three principle actions to efficiently use UNIX for their every day work.		Working with UNIX and UNIX like systems via the command line can be intimidating. The good news is a normal user only needs to have a firm understanding of three principle actions to efficiently use UNIX for their every day work.

Line 12:		Line 12:
	Where appropriate, links to external tutorials deemed suitable and apropriate to the topic are provided rather than reproducing the work here.		Where appropriate, links to external tutorials deemed suitable and apropriate to the topic are provided rather than reproducing the work here.

	==Learning to Fish or The Man Pages==		===Learning to Fish or The Man Pages===
	However, possibly even more important is being able to find information on one's own. In the spirit of this, the instructional is concluded with a detailed coverage of the built-in unix manual pages. Virtually every program installed on a UNIX like system provied a manual page for reference. Even the most proficient of UNIX users could never retain the dizzying array of programs and their options in their working memory and with the built-in manual pages, they'll never need to.		However, possibly even more important is being able to find information on one's own. In the spirit of this, the instructional is concluded with a detailed coverage of the built-in unix manual pages. Virtually every program installed on a UNIX like system provied a manual page for reference. Even the most proficient of UNIX users could never retain the dizzying array of programs and their options in their working memory and with the built-in manual pages, they'll never need to.

Line 19:		Line 19:
	A [http://www.tfug.org/helpdesk/general/man.html Beginners Guide to man Pages] is an excellent introduction into how to move around a man page easily and understand what it's telling you.		A [http://www.tfug.org/helpdesk/general/man.html Beginners Guide to man Pages] is an excellent introduction into how to move around a man page easily and understand what it's telling you.

	==POSIX Permissions==
			===POSIX Permissions===
	POSIX permissions are what determines who and to what degree users can access a file. The key terminology and function of the POSIX permission system is found on the [[UNIX Permissions]] wiki page.		POSIX permissions are what determines who and to what degree users can access a file. The key terminology and function of the POSIX permission system is found on the [[UNIX Permissions]] wiki page.

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	* newgrp		* newgrp

	==File System Navigation==
			===File System Navigation===
	The following series of tutorials provide a very basic introduction to file system navigation on unix like systems without any assumptions of prior knowledge on the topics.		The following series of tutorials provide a very basic introduction to file system navigation on unix like systems without any assumptions of prior knowledge on the topics.

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	* Copying files, moving files, removing files and directories, displaying the contents of a file, searching the contents of a file		* Copying files, moving files, removing files and directories, displaying the contents of a file, searching the contents of a file
	** [http://www.ee.surrey.ac.uk/Teaching/Unix/unix2.html Tutorial Two]		** [http://www.ee.surrey.ac.uk/Teaching/Unix/unix2.html Tutorial Two]

	====List of Utilities Covered====		====List of Utilities Covered====

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	* grep		* grep

	==File & Shell Management==
			===File & Shell Management===
	This is where your career on a UNIX type system can be made or crippled. Sure you know how to move around, list files, find out where you are, and display the contents of files. But now you have to ''do something'' with those files. And let's face it, there are a whole lot of files.		This is where your career on a UNIX type system can be made or crippled. Sure you know how to move around, list files, find out where you are, and display the contents of files. But now you have to ''do something'' with those files. And let's face it, there are a whole lot of files.

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	=Cyberduck: An SFTP client=
			==Cyberduck: An SFTP client==
	Cyberduck installs like most other mac application, just drag and drop. Please see our screen cast on using [http://ccn.ucla.edu/users/jkyle/weblog/b276e/Using_Cyberduck.html Cyberduck].		Cyberduck installs like most other mac application, just drag and drop. Please see our screen cast on using [http://ccn.ucla.edu/users/jkyle/weblog/b276e/Using_Cyberduck.html Cyberduck].

	=MacFuse installation=

			==MacFuse installation==
	#Download [http://code.google.com/p/macfuse/ MacFuse] and install it. (double click the MacFuse.mpkg file)		#Download [http://code.google.com/p/macfuse/ MacFuse] and install it. (double click the MacFuse.mpkg file)
	#Download the appropriate (tiger or leopard) sshfs from the [http://code.google.com/p/macfuse/wiki/MACFUSE_FS_SSHFS MacFuse wiki]		#Download the appropriate (tiger or leopard) sshfs from the [http://code.google.com/p/macfuse/wiki/MACFUSE_FS_SSHFS MacFuse wiki]
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	#Make sure the sshfs binary has executable permissions		#Make sure the sshfs binary has executable permissions

	==Example Workflow==		===Example Workflow===
	This assumes the user has downloaded and installed or unarchived the needed packages listed above. The below example assumes the leopard sshfs binary was downloaded.		This assumes the user has downloaded and installed or unarchived the needed packages listed above. The below example assumes the leopard sshfs binary was downloaded.
	$ tar xzvf sshfs-static-leopard.gz		$ tar xzvf sshfs-static-leopard.gz
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	$ sudo chmod +x /usr/local/bin/sshfs		$ sudo chmod +x /usr/local/bin/sshfs

	==Example Mounting of a Hoffman2 Directory==		===Example Mounting of a Hoffman2 Directory===
	Of course, you can name the /Volumes/<directory> anything you want or even put it anywhere you want. For example, I have /Volumes/Hoffman/sbook, /Volumes/Hoffman/my_home, and /Volumes/Hoffman/data		Of course, you can name the /Volumes/<directory> anything you want or even put it anywhere you want. For example, I have /Volumes/Hoffman/sbook, /Volumes/Hoffman/my_home, and /Volumes/Hoffman/data

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	=SPM=
			==SPM==
	SPM8 as well as the older SPM5 are on hoffman. In order to use these, you must add the path ("Add with Subfolders") in MATLAB.		SPM8 as well as the older SPM5 are on hoffman. In order to use these, you must add the path ("Add with Subfolders") in MATLAB.

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	=FAQ=
	==How do I change the permissions for all files I own in a certain directory?==		==FAQ==
			===How do I change the permissions for all files I own in a certain directory?===
	As a reference, please see the above section on [#File & Shell Management \| File & Shell Management]. We can do this using find and chmod.		As a reference, please see the above section on [#File & Shell Management \| File & Shell Management]. We can do this using find and chmod.
	$ find . -user myusername -type f -not -perm -g+w -exec chmod g+w {} \;		$ find . -user myusername -type f -not -perm -g+w -exec chmod g+w {} \;
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	$ fix_perms.sh		$ fix_perms.sh

	==How do I transfer data to and from hoffman?==		===How do I transfer data to and from hoffman?===
	Please see our general FAQ on how to properly transfer data between two machines found here [[FAQ#How_do_I_properly_transfer_my_data_between_two_machines_on_the_network.3F \| FAQ: How do I properly transfer my data between two machines on the network]]		Please see our general FAQ on how to properly transfer data between two machines found here [[FAQ#How_do_I_properly_transfer_my_data_between_two_machines_on_the_network.3F \| FAQ: How do I properly transfer my data between two machines on the network]]

	==How do I switch FSL Versions?==		===How do I switch FSL Versions?===
	Please see the help output of the following utility on hoffman which eases this process:		Please see the help output of the following utility on hoffman which eases this process:
	$ switch_fsl --help		$ switch_fsl --help
Line 187:		Line 196:


	=External Links=
			==External Links==
	* [http://www.ats.ucla.edu/clusters/hoffman2/faq.htm Hoffman2 FAQ (Frequently Asked Questions]		* [http://www.ats.ucla.edu/clusters/hoffman2/faq.htm Hoffman2 FAQ (Frequently Asked Questions]
	* [http://www.ats.ucla.edu/clusters/hoffman2 Hoffman2 Home Page]		* [http://www.ats.ucla.edu/clusters/hoffman2 Hoffman2 Home Page]

Elau at 22:59, 13 March 2012

2012-03-13T22:59:31Z

New page

=The Trifecta of Every Day Unix=
Working with UNIX and UNIX like systems via the command line can be intimidating. The good news is a normal user only needs to have a firm understanding of three principle actions to efficiently use UNIX for their every day work.

# POSIX Permissions
# File System Navigation
# File & Shell Management

Each of these areas require knowledge of a few small programs and how they behave. In the following sections, each program and utility is covered in detail. When appropriate, a link to the relevant wiki page on the topic is provided.

Each section is followed by an itemized list of the programs covered and some links to further information on that particular utility as well as the command to bring up the man page for the utility contained with parthesis.

Where appropriate, links to external tutorials deemed suitable and apropriate to the topic are provided rather than reproducing the work here.

==Learning to Fish or The Man Pages==
However, possibly even more important is being able to find information on one's own. In the spirit of this, the instructional is concluded with a detailed coverage of the built-in unix manual pages. Virtually every program installed on a UNIX like system provied a manual page for reference. Even the most proficient of UNIX users could never retain the dizzying array of programs and their options in their working memory and with the built-in manual pages, they'll never need to.

The man pages (for ''manual'') are the be all end all reference on UNIX systems. When reading a man page becomes natural, you know there is nothing you can't get done quickly and efficiently.

A [http://www.tfug.org/helpdesk/general/man.html Beginners Guide to man Pages] is an excellent introduction into how to move around a man page easily and understand what it's telling you.

==POSIX Permissions==
POSIX permissions are what determines who and to what degree users can access a file. The key terminology and function of the POSIX permission system is found on the [[UNIX Permissions]] wiki page.

====List of Utilities Covered====
* chmod (man chmod)
** [http://www.dartmouth.edu/~rc/help/faq/permissions.html Dartmouth Tutorial]
** Exhaustive tutorial including min-quizzes [http://www.catcode.com/teachmod/ CatCode Tutorial]
* chgrp
* umask
* newgrp

==File System Navigation==
The following series of tutorials provide a very basic introduction to file system navigation on unix like systems without any assumptions of prior knowledge on the topics.

* Listing files & directories, making directories, changing directories, the . and .. directories, pathnames, the "home" directories
** [http://www.ee.surrey.ac.uk/Teaching/Unix/unix1.html Tutorial One]
* Copying files, moving files, removing files and directories, displaying the contents of a file, searching the contents of a file
** [http://www.ee.surrey.ac.uk/Teaching/Unix/unix2.html Tutorial Two]
====List of Utilities Covered====

* ls
* mkdir
* cd
* pwd
* cp
* mv
* rm
* cat
* less
* head & tail
* grep

==File & Shell Management==
This is where your career on a UNIX type system can be made or crippled. Sure you know how to move around, list files, find out where you are, and display the contents of files. But now you have to ''do something'' with those files. And let's face it, there are a whole lot of files.

It is '''''highly recommended''''' that the reader look over [http://www.ee.surrey.ac.uk/Teaching/Unix/unix4.html Tutorial Four] on how to use wildcards for matching before preceding with this section.

The good news is, using the above utilties we just learned about we can accomplish almost anything we want to do using a very handy utility called '''''find'''''.

As the name might imply, find, well, finds things. What it finds is up to you. ''find'' has many, many options. All laid out in its man page. However, for most purposes only a few are needed. We'll cover those here.

A basic find command looks like
$ find /path/to/directory -name 'filename.txt'
This command looks at all files in /path/to/directory and in all directories therein for a file named 'filename.txt'.

====Common Options====
;-type
:Specifies the type of file we're looking for. e.g. text file, directory, link, etc.
;-name
:Specifies the name of the file. Case Sensitive
;-iname
:Specifies the name of the file. Case Insensitive
;-or
:Joins the precedeing and following terms by the boolean OR
;-and
:Joins the preceding and following terms by the boolean AND
;-not
:negates the next term. e.g. -not -empty means "is not empty"
;-exec
:excutes a shell command for each file found. The only 'trick' is to replace the actual file name with {} and end the command with a \;. This should become clear when reviewing the examples below.
;-empty
:The file or directory is empty.

We can combine the above options to preform complex searches on the file system and, even better, execute commands on those search terms. For a list of all options and their arguments, please see [http://unixhelp.ed.ac.uk/CGI/man-cgi?find Find Man Page].

====Examples====
#Find all directories named 'tsplot' in the current directory
$ find . -name tsplot -type d
#Find all empty directories in the directory /u/home9/foo/data
$ find /u/home9/foo/data -empty
#Find all empty files or directories named 'tsplot' in the current directory
$ find . -name tsplot -or -type d -empty

Using commands we've already learned to perform actions on the above.
#Find all directories named 'tsplot' in the current directory and delete them using ''rm''
$ find . -name tsplot -type d -exec rm -rf {} \;
#Find all empty directories in the directory /u/home9/foo/data and delete them
$ find . -type d -empty -exec rmdir {} \; # using rmdir for empty directories is safe as it will refuse to delete a directory with a file in it
#Find all empty files or directories named 'tsplot' in the current directory and delete them
$ find . -name tsplot -or -type d -empty -exec rm -rf {} \;

But we're not restricted to rm, of course, we can use any of the utilities we've learned about as the -exec argument.
#Find all files named design.fsf and look for a subject named 'foo'
$ find . -name design.fsf -type f -exec grep "foo" {} \;

With a little reading of the man page, we find a new option called ''-user'', which surprisingly finds all files that belong to the specified user
#Find all files owned by user 'foo' and change their permissions
$ find . -type f -user foo -exec chmod -R ug+rwX {} \;

=Setting up your Bash Profile=
This is the easiest part. Just place this one, single line in your ~/.bash_profile:
source /u/home/FMRI/apps/etc/profile

If you wish to grant group write permissions, use the umask command discussed in detail in the basic unix section above
umask 007

Or you can cut and paste this into your ~/.bash_profile
source /u/home/FMRI/apps/etc/profile
umask 007

Save, then log out and back in. This is all that is needed to gain full access to all FMRI applications. Nothing else should be put in this file, ever, unless you 100% know what you are doing and why, don't take someone else's word for it either.

=Cyberduck: An SFTP client=
Cyberduck installs like most other mac application, just drag and drop. Please see our screen cast on using [http://ccn.ucla.edu/users/jkyle/weblog/b276e/Using_Cyberduck.html Cyberduck].

=MacFuse installation=
#Download [http://code.google.com/p/macfuse/ MacFuse] and install it. (double click the MacFuse.mpkg file)
#Download the appropriate (tiger or leopard) sshfs from the [http://code.google.com/p/macfuse/wiki/MACFUSE_FS_SSHFS MacFuse wiki]
#Un-archive the downloaded sshfs (double click)
#Copy the sshfs binary to your /usr/local/bin directory or anywhere else on your path
#Make sure the sshfs binary has executable permissions

==Example Workflow==
This assumes the user has downloaded and installed or unarchived the needed packages listed above. The below example assumes the leopard sshfs binary was downloaded.
$ tar xzvf sshfs-static-leopard.gz
$ sudo mv sshfs-static-leopard /usr/local/bin/sshfs
$ sudo chmod +x /usr/local/bin/sshfs

==Example Mounting of a Hoffman2 Directory==
Of course, you can name the /Volumes/<directory> anything you want or even put it anywhere you want. For example, I have /Volumes/Hoffman/sbook, /Volumes/Hoffman/my_home, and /Volumes/Hoffman/data

# Mounting the SSH file system
$ mkdir /Volumes/MyHoffmanHome
$ sshfs your_hoffman_username@hoffman2.idre.ucla.edu:/path/to/directory/you/want/to/mount /Volumes/MyHoffmanHome -oauto_cache,reconnect

=SPM=
SPM8 as well as the older SPM5 are on hoffman. In order to use these, you must add the path ("Add with Subfolders") in MATLAB.

The path to spm8 is:
/u/home/FMRI/apps/spm8

Likewise, the path to spm5 is:
/u/home/FMRI/apps/spm5

=FAQ=
==How do I change the permissions for all files I own in a certain directory?==
As a reference, please see the above section on [#File & Shell Management | File & Shell Management]. We can do this using find and chmod.
$ find . -user myusername -type f -not -perm -g+w -exec chmod g+w {} \;

There is also a helper script which will set group permissions on all files in the current directory that are owned by user called fix_perms.sh. To use this, simply
$ fix_perms.sh

==How do I transfer data to and from hoffman?==
Please see our general FAQ on how to properly transfer data between two machines found here [[FAQ#How_do_I_properly_transfer_my_data_between_two_machines_on_the_network.3F | FAQ: How do I properly transfer my data between two machines on the network]]

==How do I switch FSL Versions?==
Please see the help output of the following utility on hoffman which eases this process:
$ switch_fsl --help
Description: switch_fsl easily and cleanly switches between various fsl versions.
Usage: switch_fsl [OPTIONS]
Options:
-h, --help Display this help/usage message
-v, --verbose Verbose output
-s, --switch VERSION Designate the appropriate fsl version.
If switching between versions 3.x and 4.x, you must log out
then back it to reset up your environment.
Available versions are: 4.0.4, 4.1.0, 4.1.1, 4.1.3
-c, --check Checks for current fsl version being used
Examples:
switch_fsl -s 4.1.0
switch_fsl --switch 4.0.4
switch_fsl -h
switch_fsl --check

=External Links=
* [http://www.ats.ucla.edu/clusters/hoffman2/faq.htm Hoffman2 FAQ (Frequently Asked Questions]
* [http://www.ats.ucla.edu/clusters/hoffman2 Hoffman2 Home Page]
* [http://www.ats.ucla.edu/clusters/hoffman2/news.htm Hoffman2 Announcements and News]
* [https://grid.ucla.edu:9443/gridsphere/gridsphere UCLA Grid Portal]
* [http://www.ats.ucla.edu/clusters/common/policies/security.htm Hoffman2 Security Policy]
* [http://www.ats.ucla.edu/clusters/grid_portal/default.htm Using the Cluster from the UCLA Grid (web) Portal]
* [http://www.ats.ucla.edu/clusters/hoffman2/head_node_access/default.htm Logging into Hoffman2 head node over SSH]
* [http://www.ats.ucla.edu/clusters/hoffman2/computing/default.htm Computing on the Hoffman2 Cluster]

Elau: /* Logging Into Hoffman (terminal vs. virtual desktop) */

2011-08-01T22:17:33Z

Logging Into Hoffman (terminal vs. virtual desktop)

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=Logging Into Hoffman (terminal vs. virtual desktop)=
There are two options for logging into Hoffman2. The first is the one you know - and which is documented elsewhere. Open up a terminal window (or terminal emulator on a PC) and use the ssh -X loginname@address to log into your favorite node. More information is available on the ATS website.

The other approach is to create a virtual session with a node on Hoffman2. This is akin to a VNC approach (implemented by ATS to work with a web-browser) but is slightly more functional. It is more powerful for anyone working remotely and it has the built in ability to keep sessions open/running even if your internet connection dies (kind of like Screens in the terminal but prettier). To use this approach you need to:

# install NX Client for your system from [http://www.nomachine.com/download.php/ www.nomachine.com/download.php]
# via terminal, log into a node of your choice on Hoffman2 and then view the contents of the Hoffman DSN key using the cat function, e.g., ssh login4; cat /etc/nxserver/client.id_dsa.key
# on your machine, launch NX Client and set up a session with the following parameters: your login name and password, address of your favorite login node (e.g., login4.hoffman2.idre.ucla.edu)
# when you go to start your session you'll have to press configure (looks different on Mac vs. PC but you can find it) - navigate to where you see a "key" button and press it
# copy and paste THE ENTIRE DSN key (produced by the cat command in step 2) to replace any text that you see in this window
# save, and log in

Once in - you are working on a linux desktop. In the bottom left (or right) you'll see a PC-style button which will display all the folders, and in Systems (I *think*) is where you'll find Terminal.

a.l.

=The Trifecta of Every Day Unix=
Working with UNIX and UNIX like systems via the command line can be intimidating. The good news is a normal user only needs to have a firm understanding of three principle actions to efficiently use UNIX for their every day work.

# POSIX Permissions
# File System Navigation
# File & Shell Management

Each of these areas require knowledge of a few small programs and how they behave. In the following sections, each program and utility is covered in detail. When appropriate, a link to the relevant wiki page on the topic is provided.

Each section is followed by an itemized list of the programs covered and some links to further information on that particular utility as well as the command to bring up the man page for the utility contained with parthesis.

Where appropriate, links to external tutorials deemed suitable and apropriate to the topic are provided rather than reproducing the work here.

==Learning to Fish or The Man Pages==
However, possibly even more important is being able to find information on one's own. In the spirit of this, the instructional is concluded with a detailed coverage of the built-in unix manual pages. Virtually every program installed on a UNIX like system provied a manual page for reference. Even the most proficient of UNIX users could never retain the dizzying array of programs and their options in their working memory and with the built-in manual pages, they'll never need to.

The man pages (for ''manual'') are the be all end all reference on UNIX systems. When reading a man page becomes natural, you know there is nothing you can't get done quickly and efficiently.

A [http://www.tfug.org/helpdesk/general/man.html Beginners Guide to man Pages] is an excellent introduction into how to move around a man page easily and understand what it's telling you.

==POSIX Permissions==
POSIX permissions are what determines who and to what degree users can access a file. The key terminology and function of the POSIX permission system is found on the [[UNIX Permissions]] wiki page.

====List of Utilities Covered====
* chmod (man chmod)
** [http://www.dartmouth.edu/~rc/help/faq/permissions.html Dartmouth Tutorial]
** Exhaustive tutorial including min-quizzes [http://www.catcode.com/teachmod/ CatCode Tutorial]
* chgrp
* umask
* newgrp

==File System Navigation==
The following series of tutorials provide a very basic introduction to file system navigation on unix like systems without any assumptions of prior knowledge on the topics.

* Listing files & directories, making directories, changing directories, the . and .. directories, pathnames, the "home" directories
** [http://www.ee.surrey.ac.uk/Teaching/Unix/unix1.html Tutorial One]
* Copying files, moving files, removing files and directories, displaying the contents of a file, searching the contents of a file
** [http://www.ee.surrey.ac.uk/Teaching/Unix/unix2.html Tutorial Two]
====List of Utilities Covered====

* ls
* mkdir
* cd
* pwd
* cp
* mv
* rm
* cat
* less
* head & tail
* grep

==File & Shell Management==
This is where your career on a UNIX type system can be made or crippled. Sure you know how to move around, list files, find out where you are, and display the contents of files. But now you have to ''do something'' with those files. And let's face it, there are a whole lot of files.

It is '''''highly recommended''''' that the reader look over [http://www.ee.surrey.ac.uk/Teaching/Unix/unix4.html Tutorial Four] on how to use wildcards for matching before preceding with this section.

The good news is, using the above utilties we just learned about we can accomplish almost anything we want to do using a very handy utility called '''''find'''''.

As the name might imply, find, well, finds things. What it finds is up to you. ''find'' has many, many options. All laid out in its man page. However, for most purposes only a few are needed. We'll cover those here.

A basic find command looks like
$ find /path/to/directory -name 'filename.txt'
This command looks at all files in /path/to/directory and in all directories therein for a file named 'filename.txt'.

====Common Options====
;-type
:Specifies the type of file we're looking for. e.g. text file, directory, link, etc.
;-name
:Specifies the name of the file. Case Sensitive
;-iname
:Specifies the name of the file. Case Insensitive
;-or
:Joins the precedeing and following terms by the boolean OR
;-and
:Joins the preceding and following terms by the boolean AND
;-not
:negates the next term. e.g. -not -empty means "is not empty"
;-exec
:excutes a shell command for each file found. The only 'trick' is to replace the actual file name with {} and end the command with a \;. This should become clear when reviewing the examples below.
;-empty
:The file or directory is empty.

We can combine the above options to preform complex searches on the file system and, even better, execute commands on those search terms. For a list of all options and their arguments, please see [http://unixhelp.ed.ac.uk/CGI/man-cgi?find Find Man Page].

====Examples====
#Find all directories named 'tsplot' in the current directory
$ find . -name tsplot -type d
#Find all empty directories in the directory /u/home9/foo/data
$ find /u/home9/foo/data -empty
#Find all empty files or directories named 'tsplot' in the current directory
$ find . -name tsplot -or -type d -empty

Using commands we've already learned to perform actions on the above.
#Find all directories named 'tsplot' in the current directory and delete them using ''rm''
$ find . -name tsplot -type d -exec rm -rf {} \;
#Find all empty directories in the directory /u/home9/foo/data and delete them
$ find . -type d -empty -exec rmdir {} \; # using rmdir for empty directories is safe as it will refuse to delete a directory with a file in it
#Find all empty files or directories named 'tsplot' in the current directory and delete them
$ find . -name tsplot -or -type d -empty -exec rm -rf {} \;

But we're not restricted to rm, of course, we can use any of the utilities we've learned about as the -exec argument.
#Find all files named design.fsf and look for a subject named 'foo'
$ find . -name design.fsf -type f -exec grep "foo" {} \;

With a little reading of the man page, we find a new option called ''-user'', which surprisingly finds all files that belong to the specified user
#Find all files owned by user 'foo' and change their permissions
$ find . -type f -user foo -exec chmod -R ug+rwX {} \;

=Setting up your Bash Profile=
This is the easiest part. Just place this one, single line in your ~/.bash_profile:
source /u/home/FMRI/apps/etc/profile

If you wish to grant group write permissions, use the umask command discussed in detail in the basic unix section above
umask 007

Or you can cut and paste this into your ~/.bash_profile
source /u/home/FMRI/apps/etc/profile
umask 007

Save, then log out and back in. This is all that is needed to gain full access to all FMRI applications. Nothing else should be put in this file, ever, unless you 100% know what you are doing and why, don't take someone else's word for it either.

=Cyberduck: An SFTP client=
Cyberduck installs like most other mac application, just drag and drop. Please see our screen cast on using [http://ccn.ucla.edu/users/jkyle/weblog/b276e/Using_Cyberduck.html Cyberduck].

=MacFuse installation=
#Download [http://code.google.com/p/macfuse/ MacFuse] and install it. (double click the MacFuse.mpkg file)
#Download the appropriate (tiger or leopard) sshfs from the [http://code.google.com/p/macfuse/wiki/MACFUSE_FS_SSHFS MacFuse wiki]
#Un-archive the downloaded sshfs (double click)
#Copy the sshfs binary to your /usr/local/bin directory or anywhere else on your path
#Make sure the sshfs binary has executable permissions

==Example Workflow==
This assumes the user has downloaded and installed or unarchived the needed packages listed above. The below example assumes the leopard sshfs binary was downloaded.
$ tar xzvf sshfs-static-leopard.gz
$ sudo mv sshfs-static-leopard /usr/local/bin/sshfs
$ sudo chmod +x /usr/local/bin/sshfs

==Example Mounting of a Hoffman2 Directory==
Of course, you can name the /Volumes/<directory> anything you want or even put it anywhere you want. For example, I have /Volumes/Hoffman/sbook, /Volumes/Hoffman/my_home, and /Volumes/Hoffman/data

# Mounting the SSH file system
$ mkdir /Volumes/MyHoffmanHome
$ sshfs your_hoffman_username@hoffman2.idre.ucla.edu:/path/to/directory/you/want/to/mount /Volumes/MyHoffmanHome -oauto_cache,reconnect

=SPM=
SPM8 as well as the older SPM5 are on hoffman. In order to use these, you must add the path ("Add with Subfolders") in MATLAB.

The path to spm8 is:
/u/home/FMRI/apps/spm8

Likewise, the path to spm5 is:
/u/home/FMRI/apps/spm5

=FAQ=
==How do I change the permissions for all files I own in a certain directory?==
As a reference, please see the above section on [#File & Shell Management | File & Shell Management]. We can do this using find and chmod.
$ find . -user myusername -type f -not -perm -g+w -exec chmod g+w {} \;

There is also a helper script which will set group permissions on all files in the current directory that are owned by user called fix_perms.sh. To use this, simply
$ fix_perms.sh

==How do I transfer data to and from hoffman?==
Please see our general FAQ on how to properly transfer data between two machines found here [[FAQ#How_do_I_properly_transfer_my_data_between_two_machines_on_the_network.3F | FAQ: How do I properly transfer my data between two machines on the network]]

==How do I switch FSL Versions?==
Please see the help output of the following utility on hoffman which eases this process:
$ switch_fsl --help
Description: switch_fsl easily and cleanly switches between various fsl versions.
Usage: switch_fsl [OPTIONS]
Options:
-h, --help Display this help/usage message
-v, --verbose Verbose output
-s, --switch VERSION Designate the appropriate fsl version.
If switching between versions 3.x and 4.x, you must log out
then back it to reset up your environment.
Available versions are: 4.0.4, 4.1.0, 4.1.1, 4.1.3
-c, --check Checks for current fsl version being used
Examples:
switch_fsl -s 4.1.0
switch_fsl --switch 4.0.4
switch_fsl -h
switch_fsl --check

==External Links==
* [http://www.ats.ucla.edu/clusters/hoffman2/faq.htm Hoffman2 FAQ (Frequently Asked Questions]
* [http://www.ats.ucla.edu/clusters/hoffman2 Hoffman2 Home Page]
* [http://www.ats.ucla.edu/clusters/hoffman2/news.htm Hoffman2 Announcements and News]
* [https://grid.ucla.edu:9443/gridsphere/gridsphere UCLA Grid Portal]
* [http://www.ats.ucla.edu/clusters/common/policies/security.htm Hoffman2 Security Policy]
* [http://www.ats.ucla.edu/clusters/grid_portal/default.htm Using the Cluster from the UCLA Grid (web) Portal]
* [http://www.ats.ucla.edu/clusters/hoffman2/head_node_access/default.htm Logging into Hoffman2 head node over SSH]
* [http://www.ats.ucla.edu/clusters/hoffman2/computing/default.htm Computing on the Hoffman2 Cluster]